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rmd13 / !Making Measurements in QuPath
Created July 8, 2020 12:14 — forked from Svidro/!Making Measurements in QuPath
Making Measurements in QuPath
Collections of scripts harvested mainly from Pete, but also picked up from the forums
Accessing dynamic measurements.groovy - Most annotation measurements are dynamically created when you click on the annotation, and
are not accessible through the standard getMeasurement function. This is a way around that.
Affine transformation.groovy - access more accurate measurements for the affine transformation used in the image alignment (m5/m6+)
Alignment of local cells.groovy - check neighborhood for similarly aligned cells
rmd13 /
Created October 28, 2019 15:12 — forked from WincerChan/
from hashlib import md5
from sqlite3 import connect as sql_conn
from time import localtime, strftime
class IllegalException(Exception):
def __init__(self, *args):
rmd13 / QuPath Memory Monitor.groovy
Created July 24, 2019 15:44 — forked from petebankhead/QuPath Memory Monitor.groovy
Groovy script to help monitor QuPath's memory use over time
* A basic GUI to help monitor memory usage in QuPath.
* This helps both to find & address out-of-memory troubles by
* 1. Showing how much memory is in use over time
* 2. Giving a button to clear the tile cache - which can be
* using up precious memory
* 3. Giving quick access to control the number of threads used
* for parallel processing
rmd13 / vid2hdf5.m
Created April 11, 2019 12:04 — forked from talmo/vid2hdf5.m
An example of converting video (MP4/AVI/MOV/etc) to HDF5
% Clean start!
clear all, clc
%% Parameters
% Path to input file
videoPath = '..\..\leap\data\examples\072212_163153.clip.mp4';
% Path to output file
% savePath = '..\..\leap\data\examples\072212_163153.clip.h5';
savePath = 'C:\tmp\072212_163153.clip.h5';
rmd13 / batchChannelMath.m
Created July 27, 2018 16:48 — forked from lacan/batchChannelMath.m
Imaris Batch Channel Math with EasyXT #Imaris #EasyXT #Matlab
% Example of looping through a folder to process a series of images.
% In this case, perform channel math.
% For convenience, this example uses EasyXT, but feel free to adapt it as needed.
% Get EasyXT Here:
% The ChannelMath method is borrowed from the XTension with the same name, made by Bitplane.
folder_name = uigetdir();
listing = dir(folder_name);